Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

(2017) Sushma Reddy et al.   SYSTEMATIC BIOLOGY

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Clustering Genes of Common Evolutionary History

(2016) Kevin Gori et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)

(2016) Serena E. Dool et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

(2016) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

Phylogenomic subsampling: a brief review

(2016) Scott V. Edwards   ZOOLOGICA SCRIPTA

PGD: a pangolin genome hub for the research community

(2016) Tze King Tan et al.   Database-The Journal of Biological Databases and Curation

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

(2015) Meng-Yun Chen et al.   SYSTEMATIC BIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

How and Why Overcome the Impediments to Resolution: Lessons from rhinolophid and hipposiderid Bats

(2014) Nicole M. Foley et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

(2013) Georgia Tsagkogeorga et al.   CURRENT BIOLOGY

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolution of the laurasiatherian phylogeny: Evidence from genomic data

(2012) Mariana F. Nery et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

(2011) Apurva Narechania et al.   Genome Biology and Evolution

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals

(2011) Björn M. Hallström et al.   PLoS One

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

Phylogenetic Utility of Nuclear Introns in Interfamilial Relationships of Caniformia (Order Carnivora)

(2011) Li Yu et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-enabled development of DNA markers for ecology, evolution and conservation

(2010) ROBERT C. THOMSON et al.   MOLECULAR ECOLOGY

Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data

(2009) Zhuo-cheng Hou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

(2008) Jena L. Chojnowski et al.   GENE

Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets

(2008) Arjun B. Prasad et al.   MOLECULAR BIOLOGY AND EVOLUTION